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A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

PLoS computational biology, 2020-08, Vol.16 (8), p.e1008030

2020

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Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007999-e1007999

2020

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Fast, accurate and simulation-free stochastic mapping

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2008-12, Vol.363 (1512), p.3985

2008

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Estimating effective population size changes from preferentially sampled genetic sequences

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007774-e1007774

2020

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Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

PLoS computational biology, 2016-03, Vol.12 (3), p.e1004789-e1004789

2016

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Predictors of Test Positivity, Mortality, and Seropositivity during the Early Coronavirus Disease Epidemic, Orange County, California, USA

Emerging infectious diseases, 2021-10, Vol.27 (10), p.2604-2618

2021

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Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

Proceedings of the National Academy of Sciences - PNAS, 2014-11, Vol.111 (44), p.E4736-E4742

2014

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Predicting B cell receptor substitution profiles using public repertoire data

PLoS computational biology, 2018-10, Vol.14 (10), p.e1006388-e1006388

2018

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Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Emerging infectious diseases, 2023-05, Vol.29 (5), p.977-987

2023

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Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori

BMC genomics, 2018-11, Vol.19 (1), p.835-835, Article 835

2018

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A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts

Biometrics, 2022-12, Vol.78 (4), p.1530-1541

2022

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High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

Proceedings of the National Academy of Sciences - PNAS, 2009-07, Vol.106 (30), p.12412-12417

2009

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Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors

Bayesian analysis, 2018-03, Vol.13 (1), p.225-252

2018

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Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Biometrics, 2020-09, Vol.76 (3), p.677-690

2020

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Counting labeled transitions in continuous-time Markov models of evolution

Journal of mathematical biology, 2008-03, Vol.56 (3), p.391-412

2008

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An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Bioinformatics, 2015-10, Vol.31 (20), p.3282-3289

2015

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Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data

Journal of computational and graphical statistics, 2017-01, Vol.26 (4), p.918-929

2017

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Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”

Biometrics, 2020-09, Vol.76 (3), p.695-699

2020

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Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking

Proceedings of the National Academy of Sciences - PNAS, 2017-07, Vol.114 (29), p.E5854-E5863

2017

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Birth/birth-death processes and their computable transition probabilities with biological applications

Journal of mathematical biology, 2018-03, Vol.76 (4), p.911-944

2018

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Estimation for General Birth-Death Processes

Journal of the American Statistical Association, 2014-06, Vol.109 (506), p.730-747

2014

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Quantifying evolutionary constraints on B-cell affinity maturation

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2015-09, Vol.370 (1676)

2015

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Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time

Journal of computational biology, 2017-05, Vol.24 (5), p.377-399

2017

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Gaussian Process‐Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies

Biometrics, 2013-03, Vol.69 (1), p.8-18

2013

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Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements

Biometrics, 2015-12, Vol.71 (4), p.1009-1021

2015

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A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts

Fast, accurate and simulation-free stochastic mapping

Estimating effective population size changes from preferentially sampled genetic sequences

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

Predictors of Test Positivity, Mortality, and Seropositivity during the Early Coronavirus Disease Epidemic, Orange County, California, USA

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

Predicting B cell receptor substitution profiles using public repertoire data

Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori

A linear noise approximation for stochastic epidemic models fit to partially observed incidence counts

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors

Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Counting labeled transitions in continuous-time Markov models of evolution

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data

Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”

Myosin-independent cytokinesis in Giardia utilizes flagella to coordinate force generation and direct membrane trafficking

Birth/birth-death processes and their computable transition probabilities with biological applications

Estimation for General Birth-Death Processes

Quantifying evolutionary constraints on B-cell affinity maturation

Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time

Gaussian Process‐Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies

Likelihood-based inference for discretely observed birth-death-shift processes, with applications to evolution of mobile genetic elements

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